In Silico Approaches and the Role of Ontologies in Aging Research

The 2013 Rostock Symposium on Systems Biology and Bioinformatics in Aging Research was again dedicated to dissecting the aging process using in silico means. A particular focus was on ontologies, as these are a key technology to systematically integrate heterogeneous information about the aging process. Related topics were databases and data integration. Other talks tackled modeling issues and applications, the latter including talks focussed on marker development and cellular stress as well as on diseases, in particular on diseases of kidney and skin

X-ray Linear Dichroism in cubic compounds: the case of Cr3+ in MgAl2O4

The angular dependence (x-ray linear dichroism) of the Cr K pre-edge in MgAl2O4:Cr3+ spinel is measured by means of x-ray absorption near edge structure spectroscopy (XANES) and compared to calculations based on density functional theory (DFT) and ligand field multiplet theory (LFM). We also present an efficient method, based on symmetry considerations, to compute the dichroism of the cubic crystal starting from the dichroism of a single substitutional site. DFT shows that the electric dipole transitions do not contribute to the features visible in the pre-edge and provides a clear vision of the assignment of the 1s-->3d transitions. However, DFT is unable to reproduce quantitatively the angular dependence of the pre-edge, which is, on the other side, well reproduced by LFM calculations. The most relevant factors determining the dichroism of Cr K pre-edge are identified as the site distortion and 3d-3d electronic repulsion. From this combined DFT, LFM approach is concluded that when the pre-edge features are more intense than 4 % of the edge jump, pure quadrupole transitions cannot explain alone the origin of the pre-edge. Finally, the shape of the dichroic signal is more sensitive than the isotropic spectrum to the trigonal distortion of the substitutional site. This suggests the possibility to obtain quantitative information on site distortion from the x-ray linear dichroism by performing angular dependent measurements on single crystals

Investigation of grain orientations of melt-textured HTSC with addition of uranium oxide, Y2O3 and Y2BaCuO5

Local grain orientations were studied in melt-textured YBCO samples processed with various amounts of depleted uranuim oxide (DU) and Y 2O3 by means of electron backscatter diffraction (EBSD) analysis. The addition of DU leads to the formation of Ucontaining nanoparticles (Y2Ba4CuUOx) with sizes of around 200 nm, embedded in the superconducting Y-123 matrix. The orientation of the Y 2BaCuO5 (Y-211) particles, which are also present in the YBCO bulk microstructure, is generally random as is the case in other melttextured Y-123 samples. The presence of Y-211 particles, however, also affects the orientation of the Y-123 matrix in these samples

Fractures osseuses et ostéodensitométrie chez l'hémodialysé

peer reviewedaudience: professiona

Primary breast lymphomas

The diagnosis, prognostic factors, and optimal management of primary breast lymphomas (PBL) is difficult. Seven patients recorded at the Geneva Cancer Registry between 1973–1998 were reviewed. Five patient had diffuse large B-cell lymphoma, one a follicular lymphoma and one a MALT-lymphoma. All patients had clinical and radiological findings consistent with breast cancer and underwent mastectomy, which is not indicated in PBL. Diagnosis should be established prior to operative interventions, as fine needle aspiration missed the diagnosis for one patient and intra-operative frozen sections for 3 patients in our study. Five-year and 10-year overall survivals were 57% and 15%, respectively. Of the 3 patients who died from PBL, 2 had tumors that were Bcl-2 positive but Bcl-6 negative. All 3 surviving patients have positive Bcl-2 and Bcl-6 immunostaining, which could be important prognostic factors if confirmed by a larger study

Methods of the ITC Four Country Smoking and Vaping Survey, wave 1 (2016)

AIM: To describe the methods of the 2016 International Tobacco Control (ITC) Four Country Smoking and Vaping (4CV) Survey, conducted in 2016 in Australia (AU), Canada (CA), England (EN) and the United States (US). METHODS: The respondents were cigarette smokers, former smokers (quit within the previous 2 years), and at-least-weekly vapers, aged 18 years and older. Eligible cohort members from the ITC Four Country Survey (4C) were retained. New respondents were sampled by commercial firms from their panels. Where possible, ages 18-24 and vapers were oversampled. Data were collected online, and respondents were remunerated. Survey weights were calibrated to benchmarks from nationally representative surveys. RESULTS: Response rates by country for new recruits once invited ranged from 15.2 to 49.6%. Sample sizes for smokers/former smokers were 1504 in AU, 3006 in CA, 3773 in EN and 2239 in the US. Sample sizes for additional vapers were 727 in CA, 551 in EN and 494 in the US. CONCLUSION: The International Tobacco Control Four Country Smoking and Vaping Survey design and data collection methods allow analyses to examine prospectively the use of cigarettes and nicotine vaping products in jurisdictions with different regulatory policies. The effects on the sampling designs and response quality of recruiting the respondents from commercial panels are mitigated by the use of demographic and geographic quotas in sampling; by quality control measures; and by the construction of survey weights taking into account smoking/vaping status, sex, age, education and geography

Pre-existing immunity to SARS-CoV-2 before the COVID-19 pandemic era in Cameroon: A comparative analysis according to HIV-status

BackgroundThe lower burden of COVID-19 in tropical settings may be due to preexisting cross-immunity, which might vary according to geographical locations and potential exposure to other pathogens. We sought to assess the overall prevalence of SARS-CoV-2 antibodies and determine SARS-CoV-2 seropositivity according to HIV-status before the COVID-19 pandemic era. MethodsA cross-sectional and comparative study was conducted at the Chantal BIYA International Reference Centre (CIRCB) on 288 stored plasma samples (163 HIV-positive versus 125 HIV-negative); all collected in 2017-2018, before the COVID-19 pandemic era. Abbott Panbio (TM) COVID-19 IgG/IgM assay was used for detecting SARS-CoV-2 immunoglobulin G (IgG) and M (IgM). Among people living with HIV (PLHIV), HIV-1 viral load and TCD4 cell count (LTCD4) were measured using Abbott Real Time PCR and BD FACSCalibur respectively. Statistical analyses were performed, with pResultsThe median [IQR] age was 25 [15-38] years. Overall seropositivity to SARS-CoV-2 antibodies was 13.5% (39/288) of which 7.3% (21) was IgG, 7.3% (21) IgM and 1.0% (3) IgG/IgM. According to HIV-status in the study population, SARS-CoV-2 seropositivity was 11.0% (18/163) among HIV-positive versus 16.8% (21/125) among HIV-negative respectively, p=0.21. Specifically, IgG was 6.1% (10/163) versus 8.8% (11/125), p=0.26; IgM was 5.5% (9/163) versus 9.6%, (12/125), p=0.13 and IgG/IgM was 0.6% (1/163) versus 1.6% (2/125) respectively. Among PLHIV, SARS-CoV-2 seropositivity according to CD4 count was 9.2% (>= 500 cells/mu L) versus 1.8% (200-499 cells/mu L), (OR=3.5; p=0.04) and 0.6% (<200 cells/mu L), (OR=17.7; p<0.01). According to viral load, SARS-CoV-2 seropositivity was 6.7% (>= 40 copies/mL) versus 4.9% (<40 copies/mL), (OR= 3.8; p<0.01). ConclusionBefore COVID-19 in Cameroon, cross-reactive antibodies to SARS-CoV-2 were in circulation, indicating COVID-19 preexisting immunity. This preexisting immunity may contribute in attenuating disease severity in tropical settings like Cameroon. Of relevance, COVID-19 preexisting immunity is lower with HIV-infection, specifically with viral replication and poor CD4-cell count. As poor CD4-count leads to lower cross-reactive antibodies (regardless of viral load), people living with HIV appear more vulnerable to COVID-19 and should be prioritized for vaccination

Humoral and cellular immune correlates of protection against COVID-19 in kidney transplant recipients.

peer reviewedAs solid organ transplant recipients are at high risk of severe COVID-19 and respond poorly to primary SARS-CoV-2 mRNA vaccination, they have been prioritized for booster vaccination. However, an immunological correlate of protection has not been identified in this vulnerable population. We conducted a prospective monocentric cohort study of 65 kidney transplant recipients who received 3 doses of BNT162b2 mRNA vaccine. Associations among breakthrough infection (BTI), vaccine responses, and patient characteristics were explored in 54 patients. Symptomatic COVID-19 was diagnosed in 32% of kidney transplant recipients during a period of 6 months after booster vaccination. During this period, SARS-CoV-2 delta and omicron were the dominant variants in the general population. Univariate Analyses identified the avidity of SARS-CoV-2 receptor binding domain binding IgG, neutralizing antibodies, and SARS-CoV-2 S2-specific interferon gamma responses as correlates of protection against BTI. No demographic or clinical parameter correlated with the risk of BTI. In multivariate analysis, the risk of BTI was best predicted by neutralizing antibody and S2-specific interferon gamma responses. In conclusion, T cell responses may help compensate for the suboptimal antibody response to booster vaccination in kidney transplant recipients. Further studies are needed to confirm these findings

Comparison of Serum HBsAg Quantitation by Four Immunoassays, and Relationships of HBsAg Level with HBV Replication and HBV Genotypes

BACKGROUND: The decline in hepatitis B virus surface antigen (HBsAg) may be an early predictor of the viral efficacy of Hepatitis B virus (HBV) therapy. The HBsAg levels obtained by different immunoassays now need comparing and the relationships between levels of HBsAg and HBV DNA alongside HBsAg and genotype must be evaluated. METHODOLOGY/PRINCIPAL FINDINGS: HBsAg levels were compared among 80 patients using the Abbott Architect assay, a commercial immunoassay approved for HBsAg detection and quantitation, and three other assays derived from immunoassays approved for HBsAg detection (manufactured by Diasorin, Bio-Rad and Roche). Good correlation was found between the Abbot vs. Diasorin, Bio-Rad and Roche assays with narrow 95% limits of agreement and small mean differences: -0.06 to 0.11, -0.09 log(10) IU/mL; -0.57 to 0.64, -0.04 log(10) IU/mL; -0.09 to 0.45, -0.27 log(10) IU/mL, respectively. These agreements were not affected by genotypes A or D. HBsAg was weakly correlated with HBV DNA, whatever the HBsAg assay used: Abbott, ρ = 0.36 p = 0.001, Diasorin ρ = 0.34, p = 0.002; Bio-Rad ρ = 0.37, p<0.001; or Roche ρ = 0.41, p<0.001. This relationship between levels of HBsAg and HBV DNA seemed to depend on genotypes. Whereas HBsAg (Abbott assay) tended to correlate with HBV DNA for genotype A (ρ = 0.44, p = 0.02), no such correlation was significant for genotypes D (ρ = 0.29, p = 0.15). CONCLUSION/SIGNIFICANCE: The quantitation of HBsAg in routine clinical samples is comparable between the reference assay and the adapted assays with acceptable accuracy limits, low levels of variability and minimum discrepancy. While HBsAg quantitation is not affected by HBV genotype, the observed association between levels of HBsAg and HBV DNA seems genotype dependent